pubmed-mcp-server

Pubmed Find Related

pubmed_find_related

Read-only

Find articles related to a source article — similar content (similar), articles citing this one (cited_by), or articles this one cites (references). Uses NCBI ELink as the primary source; falls back to Europe PMC then OpenAlex when NCBI is unavailable.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`pmid`	Yes	Source PubMed ID
`offset`	No	Result offset for pagination (0-based); page through results by incrementing by maxResults
`maxResults`	No	Maximum related articles
`relationship`	No	Relationship type: similar (content-based), cited_by (articles citing this one), references (articles this one cites)	similar

Output Schema

TableJSON Schema

Name	Required	Description
`error`	No	Present when the call failed. Absent on success.
`notice`	No	Guidance when results are empty, a fallback provider answered, offset overshot, a fallback provider could not be reached, or upstream rows were excluded for carrying no PubMed PMID. Absent on a clean NCBI result page.
`offset`	No	Result offset used
`source`	No	Provider that answered this request
`articles`	No	Related articles
`sourcePmid`	No	Source PubMed ID
`totalCount`	No	Total related articles found before windowing. A Europe PMC or OpenAlex total may shrink to the PubMed-addressable count once a request window covers the whole upstream set, since rows without a PubMed PMID cannot be returned.
`relationship`	No	Relationship type used
`coverageFailures`	No	Reference-coverage fallbacks that failed instead of answering, so the reference set is unverified rather than confirmed absent. Absent when every provider consulted answered.

Schema Changelog

Changes observed during successful MCP inspections.

Changed2 schema fields changedSep 23, 2026

changedOutput schema / properties / error / properties / data / properties / reason / description

Previous value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `europepmc_unreachable`: Europe PMC was unreachable after all retry attempts. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter). `openalex_unreachable`: OpenAlex was unreachable after all retry attempts. `openalex_invalid_response`: OpenAlex returned a body that could not be parsed (invalid JSON). `all_providers_failed`: Every provider eligible for the requested relationship failed; none answered. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `all_providers_failed`: Every provider eligible for the requested relationship failed; none answered. Other values are possible when a failure originates below the handler."

changedOutput schema / properties / error / properties / data / properties / reason / examples

Previous value: -[
-  "queue_full",
-  "ncbi_unreachable",
-  "ncbi_deadline_exceeded",
-  "ncbi_invalid_response",
-  "ncbi_resource_not_found",
-  "europepmc_unreachable",
-  "europepmc_invalid_response",
-  "europepmc_invalid_input",
-  "openalex_unreachable",
-  "openalex_invalid_response",
-  "all_providers_failed"
-]New value: +[
+  "all_providers_failed"
+]

Changed6 schema fields changedSep 11, 2026

changedOutput schema / properties / articles / items / properties / authors / description

Previous value: -"Author string"New value: +"Author string — the first three of the record's own authors, then \"et al.\". On an NCBI Bookshelf chapter these are the chapter's authors; the book's editors are in `editors`."

addedOutput schema / properties / articles / items / properties / bookTitle

Added value: +{
+  "description": "Title of the book an NCBI Bookshelf record belongs to. Present instead of `source` on a book record; absent on a journal article.",
+  "type": "string"
+}

addedOutput schema / properties / articles / items / properties / docType

Added value: +{
+  "description": "What PubMed classifies this record as: \"chapter\" or \"book\" for an NCBI Bookshelf record, \"citation\" for an ordinary journal article. Absent when PubMed supplies none.",
+  "type": "string"
+}

addedOutput schema / properties / articles / items / properties / editors

Added value: +{
+  "description": "Editors of the containing book, kept out of `authors` so they cannot displace the record's own authors. Absent on a journal article and on a book that credits no editors.",
+  "items": {
+    "description": "One editor, \"Surname Initials\" as ESummary renders it",
+    "type": "string"
+  },
+  "type": "array"
+}

addedOutput schema / properties / articles / items / properties / publisherName

Added value: +{
+  "description": "Publisher of the book an NCBI Bookshelf record belongs to. Present only on a book record; absent on a journal article.",
+  "type": "string"
+}

changedOutput schema / properties / articles / items / properties / source / description

Previous value: -"Journal source"New value: +"Journal the article appeared in. Absent on an NCBI Bookshelf record, which has no journal — its venue is in `bookTitle` and `publisherName` instead, and `docType` says which kind of record it is."

Changed3 schema fields changedSep 11, 2026

addedOutput schema / properties / coverageFailures

Added value: +{
+  "description": "Reference-coverage fallbacks that failed instead of answering, so the reference set is unverified rather than confirmed absent. Absent when every provider consulted answered.",
+  "items": {
+    "additionalProperties": false,
+    "description": "One coverage provider that could not be checked",
+    "properties": {
+      "provider": {
+        "description": "Reference-coverage provider that failed",
+        "enum": [
+          "europepmc",
+          "openalex"
+        ],
+        "type": "string"
+      },
+      "reason": {
+        "description": "Declared failure reason, e.g. europepmc_unreachable or provider_disabled",
+        "type": "string"
+      },
+      "retryable": {
+        "description": "Whether a retry can reach this provider",
+        "type": "boolean"
+      }
+    },
+    "required": [
+      "provider",
+      "reason",
+      "retryable"
+    ],
+    "type": "object"
+  },
+  "type": "array"
+}

changedOutput schema / properties / notice / description

Previous value: -"Guidance when results are empty, a fallback provider answered, offset overshot, or Europe PMC rows were excluded for carrying no PubMed PMID. Absent on a clean NCBI result page."New value: +"Guidance when results are empty, a fallback provider answered, offset overshot, a fallback provider could not be reached, or upstream rows were excluded for carrying no PubMed PMID. Absent on a clean NCBI result page."

changedOutput schema / properties / totalCount / description

Previous value: -"Total related articles found before windowing. A Europe PMC total may shrink to the PubMed-addressable count once a request window covers the whole upstream set, since rows without a PubMed PMID cannot be returned."New value: +"Total related articles found before windowing. A Europe PMC or OpenAlex total may shrink to the PubMed-addressable count once a request window covers the whole upstream set, since rows without a PubMed PMID cannot be returned."

Changed4 schema fields changedSep 9, 2026

changedOutput schema / properties / error / properties / data / properties / reason / description

Previous value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `europepmc_unreachable`: Europe PMC was unreachable after all retry attempts. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter). `openalex_unreachable`: OpenAlex was unreachable after all retry attempts. `openalex_invalid_response`: OpenAlex returned a body that could not be parsed (invalid JSON). Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `europepmc_unreachable`: Europe PMC was unreachable after all retry attempts. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter). `openalex_unreachable`: OpenAlex was unreachable after all retry attempts. `openalex_invalid_response`: OpenAlex returned a body that could not be parsed (invalid JSON). `all_providers_failed`: Every provider eligible for the requested relationship failed; none answered. Other values are possible when a failure originates below the handler."

changedOutput schema / properties / error / properties / data / properties / reason / examples

Previous value: -[
-  "queue_full",
-  "ncbi_unreachable",
-  "ncbi_deadline_exceeded",
-  "ncbi_invalid_response",
-  "ncbi_resource_not_found",
-  "europepmc_unreachable",
-  "europepmc_invalid_response",
-  "europepmc_invalid_input",
-  "openalex_unreachable",
-  "openalex_invalid_response"
-]New value: +[
+  "queue_full",
+  "ncbi_unreachable",
+  "ncbi_deadline_exceeded",
+  "ncbi_invalid_response",
+  "ncbi_resource_not_found",
+  "europepmc_unreachable",
+  "europepmc_invalid_response",
+  "europepmc_invalid_input",
+  "openalex_unreachable",
+  "openalex_invalid_response",
+  "all_providers_failed"
+]

changedOutput schema / properties / notice / description

Previous value: -"Guidance when results are empty, a fallback provider answered, or offset overshot. Absent on a clean NCBI result page."New value: +"Guidance when results are empty, a fallback provider answered, offset overshot, or Europe PMC rows were excluded for carrying no PubMed PMID. Absent on a clean NCBI result page."

changedOutput schema / properties / totalCount / description

Previous value: -"Total related articles found before windowing"New value: +"Total related articles found before windowing. A Europe PMC total may shrink to the PubMed-addressable count once a request window covers the whole upstream set, since rows without a PubMed PMID cannot be returned."

Changed6 schema fields changedAug 21, 2026

changedInput schema / $schema

Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"

addedInput schema / additionalProperties
```
Added value: +false
```

changedOutput schema / $schema

Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"

addedOutput schema / anyOf

Added value: +[
+  {
+    "not": {
+      "required": [
+        "error"
+      ]
+    },
+    "required": [
+      "sourcePmid",
+      "relationship",
+      "offset",
+      "articles",
+      "totalCount",
+      "source"
+    ]
+  },
+  {
+    "required": [
+      "error"
+    ]
+  }
+]

addedOutput schema / properties / error

Added value: +{
+  "additionalProperties": {},
+  "description": "Present when the call failed. Absent on success.",
+  "properties": {
+    "code": {
+      "description": "JSON-RPC error code for this failure.",
+      "maximum": 9007199254740991,
+      "minimum": -9007199254740991,
+      "type": "integer"
+    },
+    "data": {
+      "additionalProperties": {},
+      "properties": {
+        "reason": {
+          "description": "Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `europepmc_unreachable`: Europe PMC was unreachable after all retry attempts. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter). `openalex_unreachable`: OpenAlex was unreachable after all retry attempts. `openalex_invalid_response`: OpenAlex returned a body that could not be parsed (invalid JSON). Other values are possible when a failure originates below the handler.",
+          "examples": [
+            "queue_full",
+            "ncbi_unreachable",
+            "ncbi_deadline_exceeded",
+            "ncbi_invalid_response",
+            "ncbi_resource_not_found",
+            "europepmc_unreachable",
+            "europepmc_invalid_response",
+            "europepmc_invalid_input",
+            "openalex_unreachable",
+            "openalex_invalid_response"
+          ],
+          "type": "string"
+        },
+        "recovery": {
+          "additionalProperties": {},
+          "description": "Actionable next step for the caller.",
+          "properties": {
+            "hint": {
+              "type": "string"
+            }
+          },
+          "required": [
+            "hint"
+          ],
+          "type": "object"
+        },
+        "retryable": {
+          "description": "Whether retrying may succeed.",
+          "type": "boolean"
+        }
+      },
+      "type": "object"
+    },
+    "message": {
+      "description": "Human-readable description of what went wrong.",
+      "type": "string"
+    }
+  },
+  "required": [
+    "code",
+    "message"
+  ],
+  "type": "object"
+}

removedOutput schema / required

Removed value: -[
-  "sourcePmid",
-  "relationship",
-  "offset",
-  "articles",
-  "totalCount",
-  "source"
-]

Changed3 schema fields changedJun 11, 2026

addedOutput schema / properties / totalCount

Added value: +{
+  "description": "Total related articles found before windowing",
+  "type": "number"
+}

removedOutput schema / properties / totalFound

Removed value: -{
-  "description": "Total related articles found before windowing",
-  "type": "number"
-}

changedOutput schema / required

Previous value: -[
-  "sourcePmid",
-  "relationship",
-  "offset",
-  "articles",
-  "totalFound",
-  "source"
-]New value: +[
+  "sourcePmid",
+  "relationship",
+  "offset",
+  "articles",
+  "totalCount",
+  "source"
+]

Changed6 schema fields changedJun 9, 2026

addedInput schema / properties / offset

Added value: +{
+  "default": 0,
+  "description": "Result offset for pagination (0-based); page through results by incrementing by maxResults",
+  "maximum": 9007199254740991,
+  "minimum": 0,
+  "type": "integer"
+}

changedOutput schema / properties / notice / description

Previous value: -"Optional guidance when results are empty — e.g. invalid source PMID, or references requested for a non-PMC source. Absent on successful result pages."New value: +"Guidance when results are empty, a fallback provider answered, or offset overshot. Absent on a clean NCBI result page."

addedOutput schema / properties / offset

Added value: +{
+  "description": "Result offset used",
+  "type": "number"
+}

addedOutput schema / properties / source

Added value: +{
+  "description": "Provider that answered this request",
+  "enum": [
+    "ncbi",
+    "europepmc",
+    "openalex"
+  ],
+  "type": "string"
+}

changedOutput schema / properties / totalFound / description

Previous value: -"Total related articles found before truncation"New value: +"Total related articles found before windowing"

changedOutput schema / required

Previous value: -[
-  "sourcePmid",
-  "relationship",
-  "articles",
-  "totalFound"
-]New value: +[
+  "sourcePmid",
+  "relationship",
+  "offset",
+  "articles",
+  "totalFound",
+  "source"
+]

Changed1 schema field changedMay 16, 2026

removedOutput schema / properties / articles / items / properties / score

Removed value: -{
-  "description": "NCBI relevance score (arbitrary scale, higher = more related; only present for similar)",
-  "type": "number"
-}

Changed1 schema field changedMay 10, 2026

changedOutput schema / properties / notice / description

Previous value: -"Optional guidance when results are empty due to a known limitation — e.g. references for a non-PMC source. Absent on successful result pages."New value: +"Optional guidance when results are empty — e.g. invalid source PMID, or references requested for a non-PMC source. Absent on successful result pages."

Changed1 schema field changedApr 25, 2026

addedOutput schema / properties / notice

Added value: +{
+  "description": "Optional guidance when results are empty due to a known limitation — e.g. references for a non-PMC source. Absent on successful result pages.",
+  "type": "string"
+}

Changed1 schema field changedApr 24, 2026
- addedOutput schema / properties / articles / items / description
```
Added value: +"Related article with enriched summary"
```
Changed2 schema fields changedMar 25, 2026
- addedOutput schema / properties / articles / items / properties / pubDate
```
Added value: +{
+  "description": "Publication date",
+  "type": "string"
+}
```
- addedOutput schema / properties / articles / items / properties / source
```
Added value: +{
+  "description": "Journal source",
+  "type": "string"
+}
```
First observedMar 23, 2026

TDQS

A4.3/5.0

Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

The annotations already mark this as read-only and open-world. The description adds meaningful behavioral context beyond that: it names the primary source (NCBI ELink) and the fallback chain (Europe PMC, then OpenAlex), alerting agents that results may come from different backends and availability affects behavior. This is useful transparency not present in the annotations.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Two sentences with zero filler: the first states the core purpose and the second gives source-fallback behavior. The most important selection information is front-loaded, and every clause contributes to choosing or invoking the tool correctly.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With a complete input schema, annotations covering read-only/open-world traits, and an output schema present, the description fills the remaining need: purpose, relationship semantics, and source behavior. Nothing essential for an agent to select and invoke this tool correctly is missing.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so the schema already documents every parameter. The description mainly restates the relationship enum values that the schema already defines, adding little new semantic meaning. Baseline 3 applies because the schema carries the parameter burden.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description opens with a specific verb and resource — 'Find articles related to a source article' — and enumerates the three relationship modes (similar, cited_by, references). This clearly distinguishes it from sibling tools like pubmed_search_articles or pubmed_fetch_articles, which serve different retrieval needs.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies the natural use case: given a known PMID, retrieve related articles by content or citation links. It clearly explains the three relationship types but does not explicitly state when to avoid this tool or name an alternative for other use cases, so it misses the top-level 'when/when-not/alternatives' bar.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

All pubmed-mcp-server tools Inspect

Try in Browser

One endpoint for every MCP toolRayrun runs every MCP server behind one URL and holds the credentials. Each call is decided per client, tool, and argument, then recorded.ray.runAd

Glama MCP Gateway

Add one secure layer between your agents and this server.

Pubmed Find Related

Input Schema

Output Schema

Schema Changelog

TDQS

Glama MCP Gateway

Resources